Starting phenix.real_space_refine on Sat Apr 6 07:45:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k66_36918/04_2024/8k66_36918.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k66_36918/04_2024/8k66_36918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k66_36918/04_2024/8k66_36918.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k66_36918/04_2024/8k66_36918.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k66_36918/04_2024/8k66_36918.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k66_36918/04_2024/8k66_36918.pdb" } resolution = 2.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 34 5.16 5 Na 4 4.78 5 C 5070 2.51 5 N 1120 2.21 5 O 1386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 93": "OE1" <-> "OE2" Residue "A GLU 95": "OE1" <-> "OE2" Residue "A GLU 114": "OE1" <-> "OE2" Residue "A ARG 125": "NH1" <-> "NH2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A ARG 281": "NH1" <-> "NH2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A GLU 460": "OE1" <-> "OE2" Residue "A ARG 478": "NH1" <-> "NH2" Residue "A GLU 525": "OE1" <-> "OE2" Residue "B ARG 32": "NH1" <-> "NH2" Residue "B GLU 114": "OE1" <-> "OE2" Residue "B ARG 125": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B ARG 213": "NH1" <-> "NH2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B ARG 281": "NH1" <-> "NH2" Residue "B GLU 295": "OE1" <-> "OE2" Residue "B GLU 304": "OE1" <-> "OE2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B ARG 365": "NH1" <-> "NH2" Residue "B GLU 460": "OE1" <-> "OE2" Residue "B ARG 478": "NH1" <-> "NH2" Residue "B GLU 525": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7620 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3514 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 443, 3511 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 424} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 443, 3511 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 424} Chain breaks: 2 bond proxies already assigned to first conformer: 3595 Chain: "B" Number of atoms: 3514 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 443, 3511 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 424} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 443, 3511 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 424} Chain breaks: 2 bond proxies already assigned to first conformer: 3595 Chain: "A" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 231 Unusual residues: {' NA': 2, 'CLR': 1, 'PC1': 1, 'PTY': 1, 'T7X': 1, 'Y01': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'T7X:plan-5': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 231 Unusual residues: {' NA': 2, 'CLR': 1, 'PC1': 1, 'PTY': 1, 'T7X': 1, 'Y01': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'T7X:plan-5': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Time building chain proxies: 8.12, per 1000 atoms: 1.07 Number of scatterers: 7620 At special positions: 0 Unit cell: (104.498, 110.423, 82.4135, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 34 16.00 P 6 15.00 Na 4 11.00 O 1386 8.00 N 1120 7.00 C 5070 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG ACYS A 488 " distance=2.05 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG ACYS B 488 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.19 Conformation dependent library (CDL) restraints added in 2.5 seconds 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1668 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 2 sheets defined 77.7% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 22 through 38 removed outlier: 3.803A pdb=" N PHE A 26 " --> pdb=" O TYR A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 62 Processing helix chain 'A' and resid 72 through 85 Processing helix chain 'A' and resid 98 through 113 Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 181 through 214 Processing helix chain 'A' and resid 214 through 225 Proline residue: A 220 - end of helix Processing helix chain 'A' and resid 227 through 241 Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 258 through 273 Processing helix chain 'A' and resid 275 through 292 Processing helix chain 'A' and resid 293 through 301 removed outlier: 3.684A pdb=" N LYS A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.608A pdb=" N GLU A 305 " --> pdb=" O ASN A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 340 Processing helix chain 'A' and resid 342 through 346 Processing helix chain 'A' and resid 349 through 364 Processing helix chain 'A' and resid 373 through 377 Processing helix chain 'A' and resid 378 through 391 removed outlier: 3.564A pdb=" N LEU A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 423 Processing helix chain 'A' and resid 425 through 441 Processing helix chain 'A' and resid 441 through 448 Processing helix chain 'A' and resid 453 through 466 Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.535A pdb=" N LEU A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 500 through 516 removed outlier: 3.552A pdb=" N LEU A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 38 Processing helix chain 'B' and resid 39 through 62 Processing helix chain 'B' and resid 72 through 85 Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 98 through 113 Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 181 through 214 Processing helix chain 'B' and resid 214 through 225 Proline residue: B 220 - end of helix Processing helix chain 'B' and resid 227 through 241 Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 258 through 273 Processing helix chain 'B' and resid 275 through 292 Processing helix chain 'B' and resid 293 through 302 removed outlier: 3.599A pdb=" N LYS B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 340 Processing helix chain 'B' and resid 342 through 346 Processing helix chain 'B' and resid 349 through 364 Processing helix chain 'B' and resid 373 through 377 Processing helix chain 'B' and resid 378 through 391 removed outlier: 3.535A pdb=" N LEU B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 423 Processing helix chain 'B' and resid 425 through 441 Processing helix chain 'B' and resid 441 through 448 Processing helix chain 'B' and resid 453 through 466 Processing helix chain 'B' and resid 475 through 481 removed outlier: 3.533A pdb=" N LEU B 479 " --> pdb=" O SER B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 500 through 516 removed outlier: 3.550A pdb=" N LEU B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 396 through 397 Processing sheet with id=AA2, first strand: chain 'A' and resid 527 through 528 486 hydrogen bonds defined for protein. 1389 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1052 1.31 - 1.44: 2090 1.44 - 1.57: 4466 1.57 - 1.71: 12 1.71 - 1.84: 58 Bond restraints: 7678 Sorted by residual: bond pdb=" CA SER A 87 " pdb=" CB SER A 87 " ideal model delta sigma weight residual 1.531 1.461 0.070 1.56e-02 4.11e+03 2.04e+01 bond pdb=" CA SER B 87 " pdb=" CB SER B 87 " ideal model delta sigma weight residual 1.531 1.462 0.070 1.56e-02 4.11e+03 1.99e+01 bond pdb=" C11 T7X B 704 " pdb=" O18 T7X B 704 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C11 T7X A 603 " pdb=" O18 T7X A 603 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" N ILE A 90 " pdb=" CA ILE A 90 " ideal model delta sigma weight residual 1.458 1.496 -0.039 1.14e-02 7.69e+03 1.16e+01 ... (remaining 7673 not shown) Histogram of bond angle deviations from ideal: 98.68 - 105.74: 165 105.74 - 112.81: 4360 112.81 - 119.87: 2375 119.87 - 126.93: 3427 126.93 - 133.99: 93 Bond angle restraints: 10420 Sorted by residual: angle pdb=" O1 T7X B 704 " pdb=" P1 T7X B 704 " pdb=" O13 T7X B 704 " ideal model delta sigma weight residual 94.60 110.59 -15.99 3.00e+00 1.11e-01 2.84e+01 angle pdb=" O1 T7X A 603 " pdb=" P1 T7X A 603 " pdb=" O13 T7X A 603 " ideal model delta sigma weight residual 94.60 110.57 -15.97 3.00e+00 1.11e-01 2.83e+01 angle pdb=" O11 PTY B 705 " pdb=" P1 PTY B 705 " pdb=" O14 PTY B 705 " ideal model delta sigma weight residual 92.90 108.67 -15.77 3.00e+00 1.11e-01 2.76e+01 angle pdb=" O11 PTY A 604 " pdb=" P1 PTY A 604 " pdb=" O14 PTY A 604 " ideal model delta sigma weight residual 92.90 108.64 -15.74 3.00e+00 1.11e-01 2.75e+01 angle pdb=" O12 PC1 B 701 " pdb=" P PC1 B 701 " pdb=" O14 PC1 B 701 " ideal model delta sigma weight residual 123.67 110.29 13.38 3.00e+00 1.11e-01 1.99e+01 ... (remaining 10415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.32: 4594 32.32 - 64.63: 248 64.63 - 96.95: 35 96.95 - 129.27: 11 129.27 - 161.58: 2 Dihedral angle restraints: 4890 sinusoidal: 2308 harmonic: 2582 Sorted by residual: dihedral pdb=" C9 T7X B 704 " pdb=" C7 T7X B 704 " pdb=" C8 T7X B 704 " pdb=" O13 T7X B 704 " ideal model delta sinusoidal sigma weight residual 64.16 -134.26 -161.58 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C9 T7X A 603 " pdb=" C7 T7X A 603 " pdb=" C8 T7X A 603 " pdb=" O13 T7X A 603 " ideal model delta sinusoidal sigma weight residual 64.16 -134.27 -161.57 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" CA ILE A 300 " pdb=" C ILE A 300 " pdb=" N LYS A 301 " pdb=" CA LYS A 301 " ideal model delta harmonic sigma weight residual 180.00 158.76 21.24 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 4887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.957: 1226 0.957 - 1.914: 0 1.914 - 2.871: 0 2.871 - 3.827: 0 3.827 - 4.784: 2 Chirality restraints: 1228 Sorted by residual: chirality pdb=" C1 T7X B 704 " pdb=" C2 T7X B 704 " pdb=" C6 T7X B 704 " pdb=" O1 T7X B 704 " both_signs ideal model delta sigma weight residual False -2.42 2.37 -4.78 2.00e-01 2.50e+01 5.72e+02 chirality pdb=" C1 T7X A 603 " pdb=" C2 T7X A 603 " pdb=" C6 T7X A 603 " pdb=" O1 T7X A 603 " both_signs ideal model delta sigma weight residual False -2.42 2.36 -4.78 2.00e-01 2.50e+01 5.72e+02 chirality pdb=" CBG Y01 B 702 " pdb=" CAQ Y01 B 702 " pdb=" CBD Y01 B 702 " pdb=" CBI Y01 B 702 " both_signs ideal model delta sigma weight residual False -2.33 -2.65 0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 1225 not shown) Planarity restraints: 1202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 249 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.89e+00 pdb=" C ASN B 249 " 0.042 2.00e-02 2.50e+03 pdb=" O ASN B 249 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU B 250 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 246 " -0.030 5.00e-02 4.00e+02 4.54e-02 3.29e+00 pdb=" N PRO B 247 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 247 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 247 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 246 " 0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO A 247 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 247 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 247 " 0.021 5.00e-02 4.00e+02 ... (remaining 1199 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 85 2.58 - 3.16: 6031 3.16 - 3.74: 12201 3.74 - 4.32: 18197 4.32 - 4.90: 29062 Nonbonded interactions: 65576 Sorted by model distance: nonbonded pdb=" NH2 ARG A 478 " pdb=" O HOH A 701 " model vdw 1.997 2.520 nonbonded pdb=" O LEU A 245 " pdb=" O HOH A 702 " model vdw 2.011 2.440 nonbonded pdb=" O LEU B 86 " pdb="NA NA B 707 " model vdw 2.027 2.470 nonbonded pdb=" O HOH A 750 " pdb=" O HOH A 762 " model vdw 2.039 2.440 nonbonded pdb=" O HOH B 819 " pdb=" O HOH B 860 " model vdw 2.042 2.440 ... (remaining 65571 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 487 or resid 489 through 530 or resid 602 or re \ sid 607 through 608)) selection = (chain 'B' and (resid 22 through 487 or resid 489 through 530 or resid 702 or re \ sid 707 through 708)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 19.630 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 29.810 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 7678 Z= 0.375 Angle : 1.049 15.995 10420 Z= 0.468 Chirality : 0.199 4.784 1228 Planarity : 0.004 0.045 1202 Dihedral : 19.607 161.581 3216 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.20 % Allowed : 13.68 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.26), residues: 876 helix: 0.39 (0.19), residues: 626 sheet: None (None), residues: 0 loop : -1.86 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 285 HIS 0.002 0.001 HIS B 200 PHE 0.013 0.001 PHE B 196 TYR 0.015 0.002 TYR B 195 ARG 0.005 0.001 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 122 time to evaluate : 0.875 Fit side-chains REVERT: A 61 PHE cc_start: 0.7266 (m-10) cc_final: 0.6881 (m-80) REVERT: A 63 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7480 (mmpt) REVERT: A 185 ARG cc_start: 0.7666 (ttp-170) cc_final: 0.7234 (ttm-80) REVERT: A 304 GLU cc_start: 0.7311 (pm20) cc_final: 0.6992 (mp0) REVERT: A 414 LYS cc_start: 0.6306 (OUTLIER) cc_final: 0.6036 (tptp) REVERT: A 422 LEU cc_start: 0.8354 (tp) cc_final: 0.8146 (tp) REVERT: B 70 ARG cc_start: 0.6811 (mtm-85) cc_final: 0.6486 (mpp-170) REVERT: B 185 ARG cc_start: 0.7710 (ttp-170) cc_final: 0.7343 (ttm-80) REVERT: B 422 LEU cc_start: 0.8354 (tp) cc_final: 0.8137 (tp) outliers start: 25 outliers final: 9 residues processed: 141 average time/residue: 1.4980 time to fit residues: 221.2777 Evaluate side-chains 115 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 414 LYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 415 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN A 39 HIS A 200 HIS A 273 ASN A 421 ASN A 483 HIS B 25 ASN B 31 HIS B 39 HIS B 200 HIS ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7678 Z= 0.311 Angle : 0.640 7.208 10420 Z= 0.327 Chirality : 0.043 0.141 1228 Planarity : 0.005 0.042 1202 Dihedral : 15.157 141.523 1641 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.32 % Allowed : 14.58 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.28), residues: 876 helix: 1.35 (0.20), residues: 632 sheet: None (None), residues: 0 loop : -1.12 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 42 HIS 0.003 0.001 HIS A 483 PHE 0.014 0.002 PHE B 196 TYR 0.018 0.002 TYR A 195 ARG 0.005 0.001 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 100 time to evaluate : 0.887 Fit side-chains REVERT: A 61 PHE cc_start: 0.7289 (m-10) cc_final: 0.7027 (m-80) REVERT: A 68 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7111 (mm-30) REVERT: A 185 ARG cc_start: 0.7718 (ttp-170) cc_final: 0.7282 (ttm-80) REVERT: A 252 MET cc_start: 0.8795 (mmt) cc_final: 0.8550 (mmt) REVERT: A 304 GLU cc_start: 0.7370 (pm20) cc_final: 0.7079 (mp0) REVERT: A 422 LEU cc_start: 0.8378 (tp) cc_final: 0.8157 (tp) REVERT: B 185 ARG cc_start: 0.7718 (ttp-170) cc_final: 0.7356 (ttm-80) REVERT: B 422 LEU cc_start: 0.8381 (tp) cc_final: 0.8152 (tp) outliers start: 24 outliers final: 14 residues processed: 116 average time/residue: 1.2747 time to fit residues: 156.4982 Evaluate side-chains 112 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 486 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 7.9990 chunk 24 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7678 Z= 0.169 Angle : 0.514 6.105 10420 Z= 0.267 Chirality : 0.038 0.128 1228 Planarity : 0.004 0.040 1202 Dihedral : 13.967 130.897 1624 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.69 % Allowed : 14.83 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.29), residues: 876 helix: 2.01 (0.20), residues: 634 sheet: None (None), residues: 0 loop : -0.92 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 285 HIS 0.002 0.000 HIS A 39 PHE 0.013 0.001 PHE B 196 TYR 0.015 0.002 TYR A 195 ARG 0.006 0.001 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 0.872 Fit side-chains REVERT: A 61 PHE cc_start: 0.7178 (m-10) cc_final: 0.6788 (m-80) REVERT: A 68 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7073 (mm-30) REVERT: A 70 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.7181 (ptp90) REVERT: A 185 ARG cc_start: 0.7685 (ttp-170) cc_final: 0.7304 (ttm-80) REVERT: A 304 GLU cc_start: 0.7368 (pm20) cc_final: 0.7076 (mp0) REVERT: A 422 LEU cc_start: 0.8339 (tp) cc_final: 0.8135 (tp) REVERT: A 529 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9110 (mp) REVERT: B 70 ARG cc_start: 0.6956 (mpp80) cc_final: 0.6755 (mpp-170) REVERT: B 185 ARG cc_start: 0.7691 (ttp-170) cc_final: 0.7349 (ttm-80) REVERT: B 422 LEU cc_start: 0.8349 (tp) cc_final: 0.8135 (tp) REVERT: B 529 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9116 (mp) outliers start: 19 outliers final: 7 residues processed: 119 average time/residue: 1.3672 time to fit residues: 171.4716 Evaluate side-chains 110 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 529 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 76 optimal weight: 5.9990 chunk 22 optimal weight: 0.0770 chunk 70 optimal weight: 2.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7678 Z= 0.156 Angle : 0.503 5.899 10420 Z= 0.260 Chirality : 0.038 0.122 1228 Planarity : 0.004 0.046 1202 Dihedral : 13.146 125.758 1620 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.30 % Allowed : 14.96 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.29), residues: 876 helix: 2.22 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -0.80 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 285 HIS 0.001 0.000 HIS A 200 PHE 0.013 0.001 PHE B 196 TYR 0.015 0.002 TYR B 195 ARG 0.009 0.001 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 0.819 Fit side-chains REVERT: A 61 PHE cc_start: 0.7102 (m-10) cc_final: 0.6612 (m-80) REVERT: A 68 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7005 (mm-30) REVERT: A 70 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.7162 (ptp90) REVERT: A 185 ARG cc_start: 0.7684 (ttp-170) cc_final: 0.7279 (ttm-80) REVERT: A 304 GLU cc_start: 0.7375 (pm20) cc_final: 0.7080 (mp0) REVERT: A 422 LEU cc_start: 0.8296 (tp) cc_final: 0.8095 (tp) REVERT: B 185 ARG cc_start: 0.7688 (ttp-170) cc_final: 0.7348 (ttm-80) REVERT: B 422 LEU cc_start: 0.8317 (tp) cc_final: 0.8113 (tp) outliers start: 16 outliers final: 8 residues processed: 115 average time/residue: 1.4322 time to fit residues: 173.3410 Evaluate side-chains 114 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 301 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.0020 chunk 1 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 0 optimal weight: 0.8980 chunk 43 optimal weight: 0.0070 chunk 76 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 0.4606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN B 421 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7678 Z= 0.132 Angle : 0.474 5.798 10420 Z= 0.246 Chirality : 0.037 0.120 1228 Planarity : 0.004 0.041 1202 Dihedral : 12.687 127.203 1620 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.79 % Allowed : 15.86 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.29), residues: 876 helix: 2.40 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -0.74 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 285 HIS 0.001 0.000 HIS A 200 PHE 0.013 0.001 PHE B 196 TYR 0.014 0.002 TYR B 195 ARG 0.008 0.001 ARG B 528 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 0.887 Fit side-chains REVERT: A 61 PHE cc_start: 0.6985 (m-10) cc_final: 0.6412 (m-80) REVERT: A 68 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7009 (mm-30) REVERT: A 70 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.7096 (ptp90) REVERT: A 185 ARG cc_start: 0.7664 (ttp-170) cc_final: 0.7263 (ttm-80) REVERT: A 304 GLU cc_start: 0.7349 (pm20) cc_final: 0.7049 (mp0) REVERT: B 185 ARG cc_start: 0.7675 (ttp-170) cc_final: 0.7343 (ttm-80) outliers start: 12 outliers final: 6 residues processed: 112 average time/residue: 1.4769 time to fit residues: 173.7730 Evaluate side-chains 105 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.0030 chunk 16 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 0.0980 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 0.1980 chunk 44 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7678 Z= 0.116 Angle : 0.453 6.069 10420 Z= 0.234 Chirality : 0.036 0.117 1228 Planarity : 0.004 0.040 1202 Dihedral : 12.197 128.559 1620 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.41 % Allowed : 16.37 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.29), residues: 876 helix: 2.61 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -0.67 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 285 HIS 0.001 0.000 HIS A 200 PHE 0.012 0.001 PHE B 196 TYR 0.013 0.001 TYR A 195 ARG 0.009 0.001 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 0.823 Fit side-chains REVERT: A 32 ARG cc_start: 0.7225 (mpt-90) cc_final: 0.7000 (mtp85) REVERT: A 70 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.6889 (ptp90) REVERT: A 185 ARG cc_start: 0.7660 (ttp-170) cc_final: 0.7267 (ttm-80) REVERT: A 304 GLU cc_start: 0.7353 (pm20) cc_final: 0.7018 (mp0) REVERT: A 422 LEU cc_start: 0.8276 (tp) cc_final: 0.8062 (tp) REVERT: B 185 ARG cc_start: 0.7663 (ttp-170) cc_final: 0.7336 (ttm-80) REVERT: B 422 LEU cc_start: 0.8255 (tp) cc_final: 0.8043 (tp) outliers start: 9 outliers final: 6 residues processed: 111 average time/residue: 1.4156 time to fit residues: 165.3645 Evaluate side-chains 107 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.9990 chunk 48 optimal weight: 0.0770 chunk 62 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 84 optimal weight: 0.0870 chunk 53 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7678 Z= 0.142 Angle : 0.489 7.168 10420 Z= 0.252 Chirality : 0.037 0.157 1228 Planarity : 0.004 0.044 1202 Dihedral : 12.212 124.116 1620 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.05 % Allowed : 15.73 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.29), residues: 876 helix: 2.56 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -0.66 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 499 HIS 0.001 0.000 HIS A 200 PHE 0.013 0.001 PHE B 196 TYR 0.015 0.002 TYR A 195 ARG 0.010 0.001 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 0.858 Fit side-chains REVERT: A 32 ARG cc_start: 0.7280 (mpt-90) cc_final: 0.7047 (mtp85) REVERT: A 185 ARG cc_start: 0.7669 (ttp-170) cc_final: 0.7273 (ttm-80) REVERT: A 304 GLU cc_start: 0.7383 (pm20) cc_final: 0.7026 (mp0) REVERT: A 422 LEU cc_start: 0.8282 (tp) cc_final: 0.8081 (tp) REVERT: B 185 ARG cc_start: 0.7675 (ttp-170) cc_final: 0.7341 (ttm-80) REVERT: B 295 GLU cc_start: 0.7718 (mp0) cc_final: 0.7503 (mp0) REVERT: B 304 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6967 (pm20) REVERT: B 422 LEU cc_start: 0.8287 (tp) cc_final: 0.8080 (tp) outliers start: 14 outliers final: 9 residues processed: 113 average time/residue: 1.3901 time to fit residues: 165.5507 Evaluate side-chains 113 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 304 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 53 optimal weight: 0.0870 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7678 Z= 0.163 Angle : 0.515 7.853 10420 Z= 0.265 Chirality : 0.038 0.150 1228 Planarity : 0.004 0.043 1202 Dihedral : 12.383 120.616 1620 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.66 % Allowed : 16.24 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.29), residues: 876 helix: 2.46 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -0.70 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 499 HIS 0.002 0.000 HIS A 200 PHE 0.013 0.001 PHE B 196 TYR 0.016 0.002 TYR A 195 ARG 0.009 0.001 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 109 time to evaluate : 0.856 Fit side-chains REVERT: A 185 ARG cc_start: 0.7684 (ttp-170) cc_final: 0.7286 (ttm-80) REVERT: A 304 GLU cc_start: 0.7393 (pm20) cc_final: 0.7076 (mp0) REVERT: B 185 ARG cc_start: 0.7683 (ttp-170) cc_final: 0.7346 (ttm-80) REVERT: B 295 GLU cc_start: 0.7737 (mp0) cc_final: 0.7492 (mp0) outliers start: 11 outliers final: 9 residues processed: 116 average time/residue: 1.3666 time to fit residues: 167.1927 Evaluate side-chains 115 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 83 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7678 Z= 0.154 Angle : 0.505 7.896 10420 Z= 0.260 Chirality : 0.038 0.144 1228 Planarity : 0.004 0.042 1202 Dihedral : 12.343 121.626 1620 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.41 % Allowed : 17.01 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.28), residues: 876 helix: 2.46 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -0.75 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 499 HIS 0.002 0.000 HIS A 200 PHE 0.013 0.001 PHE B 196 TYR 0.015 0.002 TYR A 195 ARG 0.009 0.001 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 0.897 Fit side-chains REVERT: A 32 ARG cc_start: 0.7272 (mpt-90) cc_final: 0.7035 (mtp85) REVERT: A 185 ARG cc_start: 0.7678 (ttp-170) cc_final: 0.7275 (ttm-80) REVERT: A 304 GLU cc_start: 0.7398 (pm20) cc_final: 0.7078 (mp0) REVERT: B 185 ARG cc_start: 0.7687 (ttp-170) cc_final: 0.7350 (ttm-80) REVERT: B 295 GLU cc_start: 0.7728 (mp0) cc_final: 0.7483 (mp0) outliers start: 9 outliers final: 8 residues processed: 113 average time/residue: 1.3863 time to fit residues: 165.6806 Evaluate side-chains 117 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.0030 chunk 39 optimal weight: 0.9980 chunk 58 optimal weight: 0.0170 chunk 87 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 overall best weight: 0.4628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7678 Z= 0.134 Angle : 0.484 7.692 10420 Z= 0.248 Chirality : 0.037 0.137 1228 Planarity : 0.004 0.041 1202 Dihedral : 12.215 123.338 1620 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.28 % Allowed : 16.75 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.29), residues: 876 helix: 2.56 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -0.74 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 499 HIS 0.001 0.000 HIS A 200 PHE 0.013 0.001 PHE B 196 TYR 0.014 0.002 TYR A 195 ARG 0.010 0.001 ARG B 528 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 0.913 Fit side-chains REVERT: A 32 ARG cc_start: 0.7277 (mpt-90) cc_final: 0.7044 (mtp85) REVERT: A 185 ARG cc_start: 0.7656 (ttp-170) cc_final: 0.7264 (ttm-80) REVERT: A 304 GLU cc_start: 0.7397 (pm20) cc_final: 0.7077 (mp0) REVERT: B 185 ARG cc_start: 0.7680 (ttp-170) cc_final: 0.7347 (ttm-80) REVERT: B 295 GLU cc_start: 0.7708 (mp0) cc_final: 0.7502 (mp0) outliers start: 8 outliers final: 8 residues processed: 111 average time/residue: 1.3765 time to fit residues: 161.2994 Evaluate side-chains 117 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 10 optimal weight: 0.1980 chunk 19 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 0.0010 chunk 3 optimal weight: 1.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.125847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.097205 restraints weight = 13762.958| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.62 r_work: 0.2809 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7678 Z= 0.149 Angle : 0.499 8.002 10420 Z= 0.256 Chirality : 0.037 0.140 1228 Planarity : 0.004 0.043 1202 Dihedral : 12.229 122.459 1620 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.41 % Allowed : 16.62 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.28), residues: 876 helix: 2.51 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -0.75 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 499 HIS 0.001 0.000 HIS A 200 PHE 0.013 0.001 PHE B 196 TYR 0.015 0.002 TYR A 195 ARG 0.010 0.001 ARG A 528 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3723.26 seconds wall clock time: 68 minutes 8.12 seconds (4088.12 seconds total)